"We're well-aware of China's militarization of the South China Sea," Sanders told reporters. "There will be near-term and long-term consequences."

The Pentagon also weighed in on the development.

"We have been very vocal about our concerns about them militarizing these artificial islands," Defense Department spokeswoman Dana White said. "China has to realize that they have benefited from the free navigation of the sea and the U.S. Navy has been the guarantor of that."

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White House: We're well aware of China's militarization of the South China Sea

China quietly installed anti-ship cruise missiles and surface-to-air missile systems on three of its fortified outposts in the South China Sea, a move that allows Beijing to further project its power in the hotly disputed waters, sources with direct knowledge of U.S. intelligence reports had told CNBC.

Intelligence assessments say the missile platforms were deployed to Fiery Cross Reef, Subi Reef and Mischief Reef in the Spratly Islands within the past 30 days, according to the sources who spoke on the condition of anonymity.

The placement of the defensive weapons also comes on the heels of China's recent South China Sea installation of military jamming equipment, which disrupts communications and radar systems.

The Spratlys, to which six countries lay claim, are located approximately two-thirds of the way east from southern Vietnam to the southern Philippines.

Map of the South China Sea.

CSIS Asia Maritime Transparency Initiative/CNBC

The new coastal defense systems represent a significant addition to China's military portfolio in one of the most contested regions in the world.

The South China Sea, which is home to more than 200 specks of land, serves as a gateway to global sea routes where approximately $3.4 trillion of trade passes annually.

The numerous overlapping sovereign claims to islands, reefs and rocks — many of which disappear under high tide — have turned the waters into an armed camp. Beijing holds the lion's share of these features with approximately 27 outposts peppered throughout.

The United States has remained neutral – but expressed concern – about the overlapping sovereignty claims to the Spratlys.

"The biggest dilemma is that Beijing could over time deploy many more missiles than Washington's naval missile defense platforms could defend against," Harry Kazianis, director of defense studies at the Center for the National Interest, told CNBC.

"At the end of the day, for Beijing, simple math means they would win a short-term military engagement and that spells all sorts of trouble for the U.S. Navy," he added.

"This should be seen as China crossing an important threshold. Missile platforms present a clear offensive threat," Gregory Poling, Center for Strategic and International Studies fellow and director of the Asia Maritime Transparency Initiative, told CNBC.